Biodiversity may be positively related to crop yield, but the mechanisms by which such effects are realized are as yet poorly understood. Reduced pest incidence may be one cause. To better predict the quality and strength of biodiversity effects in cacao agroforestry systems and to disentangle potential drivers, we analyzed relationships of plant diversity with crop quantity (yield, fruit set, fruit size), pathogen incidence (Moniliophthora perniciosa, Moniliophthora roreri, Phytophthora spp.), and with the profile of selected secondary compounds (methylxanthines and polyphenols) in seeds of 48 cacao trees cultivated on 14 farms in Peruvian Amazonia. Our results revealed no correlation of yield per hectare or total fruit set with plant alpha diversity measures on the studied cacao farms. However, the number and size of ripe fruits without fungal infestation increased at higher diversity of the herb and shrub layer and at lower diversity and smaller basal area of shade trees. Greater diversity in the herb and shrub layer reduced the incidence of the Phytophthora pathogen but increased the incidence of M. roreri. At higher alpha diversity in the understory, contents of caffeine, theobromine, and catechin hydrate in cacao seeds significantly increased. The changes in plant secondary compounds showed inconsistent relations with the infestation rates of fungal pathogens. While trees infested with M. perniciosa showed higher contents of polyphenols and caffeine in seeds, cacao trees with higher caffeine content in seeds were less likely to be affected by Phytophthora. Similarly, a higher epicatechin content in seeds was associated with reduced M. roreri incidence. Our data provide evidence for a tight interplay of biodiversity, pathogen incidence, and the crop's secondary metabolism on cacao farms. Overall, considering biochemical traits in yield-diversity relationships allowed for a better understanding of the contribution of biotic interactions to biodiversity effects in tropical agroforestry systems.